Changes in the longitudinal relaxation rate (R1) may play a role in the MRI signal intensity increases that have been associated with physiological brain activation. We used gradient-echo echo-planar MRI (GRE-EPI) to test whether physiological activations associated with hypercapnia in dogs were dependent on the delay (TR) between successive images in a time-series. Our results show that, in addition to activation-induced changes in the R2∗ (transverse relaxation including inhomogeneity effects), activation-induced changes in R1 are significant under certain pulsing conditions. In our paradigm, the R1 contribution became significant at TR values of 1 s or less.